Assume that you receive many incoming instant messages (IM) in Microsoft Lync 2013 (Skype for Business) with tabbed or non-tabbed IM conversation mode. The taskbar icon only flashes for the first time when the IM arrives. It doesn't flash for the next immediate messages.
Note This behavior doesn't apply to the IMs that are received after around 30 seconds of the first IM. After that, any IM will be displayed in a new section in the IM window, and the taskbar icon will also flash.
To fix this issue, install the November 1, 2016, update (KB3127934) for Lync 2013 (Skype for Business).
Note Lync 2013 was upgraded to Skype for Business in April 2015.